Rei turns around and faces the camera.
Shinji is reflected in the extreme close-up of her eye.
Kendrix: This is the point where he cries. Maybe his mention of "smiling" (something she had only done for Gendo untill this point) made her think of his father, maybe it was just the similar pose and strong family resemblance, Shinji is pretty much his old man's spitting image.
Whatever the exact reason may be, Rei didn't realize the similarity of this situation and the activation experiment until now, which is why she is so visibly shocked. She's thinking something amongst the lines of "How could I miss this?!" Note that she's already slightly blushing at this point.
